As far as the colors go, the colors for tray buttons is controlled by TrayButtonStyle, which was an undocumented feature, so probably not used (it's documented now though). It used to be the case that when a setting wasn't in TrayButtonStyle, the colors for tray buttons would come from TaskListStyle, but that was really a pretty arbitrary choice as mentioned in issue #61. Now the defaults come from TrayStyle instead and so the tray buttons will look just like the tray if their settings are not overridden explicitly. It's also now possible to specify gradients and ActiveBackground/ActiveForeground in TrayStyle though. So one way to fix this would be to move the settings from TaskListStyle to TrayStyle. Another option would be to simply duplicate them in TrayButtonStyle.
I have to admit that I'm not completely happy with the way this works right now. In a way it seems odd that the background color for tray buttons would come from the tray itself, but that does make sense for flat buttons, so maybe it's ok. I think this makes more sense than having TrayButtonStyle take defaults from TaskListStyle.
As far as the image scaling is concerned, it was broken before. For icons that are wider than they are tall, it wouldn't have made much difference (as can be seen here), but for icons that were too tall, it was pretty obvious that the scaling was broken. The height of the dog icon should match the height of the other icons now. Going forward, there are probably a couple more pixels I could allow icons to use in trays and perhaps it should be a percentage rather than a fixed amount so that things look right at high resolutions.